memex — temporal knowledge graph memory for AI coding agents

<!-- mcp-name: io.github.stifler7/memex -->

Persistent memory and codebase context for AI coding agents, served over MCP. A bitemporal knowledge graph of your repository — modules, symbols, decisions, problems — for Claude Code, Cursor, Codex, Gemini CLI, and any MCP-compatible agent.

A daemon and MCP server that turns every commit and every file change into structured graph state: modules, symbols, decisions, problems, lockfile facts. Sessions stop starting blind. Agents stop re-discovering the same refactor every time you /clear.

flowchart LR
    A[Your repository<br/>files + git] --> B[memex watcher<br/>tree-sitter + Gemini]
    B --> C[Neo4j graph<br/>bitemporal facts]
    C --> D[MCP server<br/>stdio / HTTP]
    D --> E[AI agent<br/>Claude · Cursor · Codex · Gemini CLI]
    E -.->|writes decisions back| C

    style B fill:#cfe8ff,stroke:#0066cc,color:#000
    style C fill:#fff4cf,stroke:#cc9900,color:#000
    style E fill:#d4f5d4,stroke:#2d8f2d,color:#000

Install

Via Claude Code marketplace

/plugin marketplace add STiFLeR7/claude-plugins
/plugin install memex-mcp@stifler-marketplace

Restart your Claude Code session.

Manual

docker compose -f docker/docker-compose.yml up -d
cat > .env <<EOF
NEO4J_URI=bolt://localhost:7687
NEO4J_USER=neo4j
NEO4J_PASSWORD=memex-local
GEMINI_API_KEY=your-key-here
EOF
npx stifler-memex-mcp init --repo .
npx stifler-memex-mcp watch --repo .
npx stifler-memex-mcp serve --repo .

Channel	Command
Claude Code marketplace	/plugin install memex-mcp@stifler-marketplace
npx (no install)	npx stifler-memex-mcp <cmd>
uv	uv add memex-mcp
pip	pip install memex-mcp
source	git clone github.com/STiFLeR7/memex && uv sync

At a glance

Property	Value
Output	A Neo4j graph populated continuously from your repo
Storage	Neo4j via Graphiti. Bitemporal — every edge has created_at and optional expired_at
Survives	/clear, terminal crashes, machine restarts, teammate handoffs
Hands off to	Claude Code, Cursor, Codex, Gemini CLI, any MCP client
Granularity	Scales from 50 to 5000+ modules via hierarchical Leiden clusters
Synthesis	Gemini Flash distills commits into Decision nodes; Pro for grounded synthesis
Confidence	Computed at query time. Two-regime decay (validated half-life ~139d, unvalidated stale at 30d)
Write governance	Per-node-type ACL, intent-confirmation on agent writes, explicit corroborates / supersedes semantics
Tests	333 passing, ~93% coverage

The lifecycle

flowchart TD
    Init[memex init<br/>extract baseline] --> Watch[memex watch<br/>daemon + git hooks]
    Watch -->|commit| Extract[tree-sitter extract<br/>symbols, imports, lockfile]
    Extract --> Synth[Gemini Flash<br/>diff → Decision nodes]
    Synth --> Write[Graphiti add_episode<br/>+ post-hoc bitemporal SET]
    Write --> Decay[Scheduler<br/>nightly confidence decay]
    Decay -->|stale edges| Archive[expired_at = now]

    Serve[memex serve<br/>MCP stdio/HTTP] -.->|reads| Write
    Agent[AI agent] -->|14 MCP tools| Serve
    Serve -->|record_decision / record_problem| Write

    Cluster[memex cluster<br/>Leiden over hybrid edges] -.->|every N commits| Write

    style Init fill:#e8f4ff,color:#000
    style Watch fill:#fff4cf,color:#000
    style Synth fill:#ffe0cc,color:#000
    style Serve fill:#d4f5d4,color:#000

MCP tools

14 tools — eight read, four write, two analytic.

Read

Tool	When
get_project_context	Session start. Returns a cluster-level briefing under 1500 tokens regardless of repo size
get_symbol_context	Before editing a function or class. Returns callers, callees, linked decisions
get_recent_decisions	Last N days of architectural decisions, optionally module-scoped
get_open_problems	Active bugs and tech debt, sorted by severity
search_context	Hybrid search: semantic × keyword × graph traversal × RRF merge
get_stale_context	Edges whose composite confidence dropped below threshold
explain_change	Given a commit SHA, cross-references the diff with linked Decision/Problem nodes and asks Gemini Pro for a grounded explanation
predict_impact	Given a file path, returns a ranked list of modules likely affected based on graph coupling (no LLM call)

Write

Tool	When
record_decision	After making a technical choice. Supports corroborates (reinforce) and supersedes (replace)
record_problem	When discovering a bug or piece of tech debt
resolve_problem	When a tracked problem is fixed
invalidate_edge	When a stored fact is no longer true

Bitemporal confidence

Confidence is not a stored number that mutates. It is computed at query time from base_confidence, validation status, time since last reinforcement, and access count.

flowchart LR
    Edge[Edge created<br/>base_confidence] --> Q{Validated by<br/>a human?}
    Q -->|yes| Slow[Slow regime<br/>half-life ~139d]
    Q -->|no| Fast[Fast regime<br/>stale at exactly 30d]
    Slow --> Score[Composite score<br/>conf × recency × rehearsal]
    Fast --> Score
    Score -->|below floor| Stale[get_stale_context surfaces it]
    Score -->|access| Bump[last_reinforced_at updated]
    Bump --> Score

    style Slow fill:#d4f5d4,color:#000
    style Fast fill:#ffd4d4,color:#000

Property	Value
Validated half-life	~139 days
Unvalidated stale threshold	30 days (composite < 0.3)
Recency τ	90 days (exponential decay)
Composite formula	conf × recency × (1 + rehearsal_w × log(1 + access_count))
Conflict similarity threshold	0.4 (below this + overlapping validity = conflict)
Intent-confirmation threshold	0.85 (MCP write similarity check)

Hierarchical clusters

memex cluster runs hierarchical Leiden over a hybrid edge graph:

Edge type	Weight
Directory co-location	1.0
Module imports	2.0
Symbol calls	log(1 + calls)

Property	Value
Algorithm	graspologic.partition.hierarchical_leiden with fixed seed
Naming	TF-IDF top-3 over module docstrings + symbol names, parent-dir fallback
ID pinning	Jaccard ≥ 0.5 across reruns (cluster names stay stable through renames)
User overrides	.memex/clusters.yaml — any assignment can be locked
Context budget	get_project_context stays under 1500 tokens whether your repo has 50 or 5000 modules

Connect your agent

<details> <summary><b>Claude Code</b></summary>

Marketplace install above does this for you. Manual wiring in .claude/settings.json:

{
  "mcpServers": {
    "memex": {
      "type": "stdio",
      "command": "npx",
      "args": ["-y", "stifler-memex-mcp", "serve", "--repo", "."]
    }
  }
}

</details>

<details> <summary><b>Cursor</b></summary>

Add to ~/.cursor/mcp.json:

{
  "mcpServers": {
    "memex": {
      "command": "npx",
      "args": ["-y", "stifler-memex-mcp", "serve", "--repo", "."]
    }
  }
}

</details>

<details> <summary><b>Gemini CLI</b></summary>

Add to ~/.gemini/settings.json:

{
  "mcpServers": {
    "memex": {
      "command": "npx",
      "args": ["-y", "stifler-memex-mcp", "serve", "--repo", "."]
    }
  }
}

</details>

<details> <summary><b>Codex</b></summary>

Add to ~/.codex/config.toml:

[mcp_servers.memex]
command = "npx"
args = ["-y", "stifler-memex-mcp", "serve", "--repo", "."]

</details>

<details> <summary><b>Anthropic memory tool (memory_20250818)</b></summary>

memex can back Claude's native memory tool — agents read from a per-session graph projection plus a writable scratch zone.

memex memory-tool serve --repo .                     # in-process
memex memory-tool serve --repo . --transport http    # FastAPI on :7464

from memex.memory_tool import MemexAsyncMemoryTool
memory_tool = MemexAsyncMemoryTool(repo_root=".")
client.beta.messages.run_tools(..., tools=[memory_tool])

</details>

Operating principles

#	Principle	The bet
1	Bitemporal, never destructive	Edges are expired, not deleted. WHERE r.expired_at IS NULL filters live state
2	Confidence is computed, not stored	Mutating a number invites silent drift. Recompute every read
3	Two regimes for decay	Validated facts decay slowly; unvalidated facts must earn their place by being accessed
4	Human in the loop	memex review queues lowest-confidence Decision nodes for explicit validation
5	Write governance	Per-node-type ACL. Decision.policy = open, Module.policy = locked. Intent-confirmation on similar-content writes
6	Tokens are budgeted	get_project_context stays under 1500 tokens at any repo size via Leiden clusters
7	Synthesis only on commits	The watcher batches by debounce window. Gemini Flash is not in the hot path of a tool call
8	Pro for synthesis, Flash for extraction	explain_change uses Pro because grounding matters. Everything else uses Flash
9	Multi-repo aware	One watcher + one MCP server can manage hundreds of repos. --repo switches scope
10	Local-first	Neo4j runs in your Docker. Gemini is the only outbound call, and only on commits

When to use memex

Use it when	Skip it when
Multi-week or multi-month project	One-shot script, throwaway prototype
You work across multiple agents (Claude, Cursor, Codex) and want shared context	You only ever pair with one agent on one task
Architectural decisions are made over time and need to be remembered	The whole project fits in a single 200k-token context window
You want to query "what did we decide about X" from any session	Your repo is already small enough to paste into the prompt
Multiple developers using AI agents on the same codebase	Solo work where you never /clear

Project structure

memex/
├── memex/
│   ├── extractor/        tree-sitter + lockfile parsers
│   ├── graph/            Neo4j writes, confidence, archive, cluster engine
│   ├── synthesizer/      Gemini Flash → Decision nodes
│   ├── mcp_server/       14 MCP tools (read + write + analytic)
│   ├── memory_tool/      Anthropic memory_20250818 adapter
│   ├── watcher/          daemon + git hooks
│   └── cli.py            init / watch / serve / review / graph / cluster
├── tests/                333 passing, ~93% coverage
├── docker/               Neo4j compose
├── npm/                  npx wrapper (publishes as stifler-memex-mcp)
└── Dockerfile            introspection-only image for MCP directory sandboxes

Commands

Command	What it does
memex init	Extract baseline graph state, run first cluster pass
memex watch	Daemon that listens for file + git events and writes to Neo4j
memex serve	Run the MCP server (stdio, HTTP, or both)
memex review	TUI that walks lowest-confidence decisions for human validation
memex graph --output graph.html	Self-contained D3 force layout with cluster overlays
memex cluster [--rerun] [--dry-run]	Run Leiden over the hybrid edge graph; pin cluster IDs by Jaccard ≥ 0.5
memex memory-tool serve	Back Anthropic's memory_20250818 tool with a graph projection

License

MIT. See LICENSE.

Author

Hill Patel (@STiFLeR7)

Core Contributors & Maintainers

• Hill Patel (@STiFLeR7) — architect, maintainer
• Nirvaan Lagishetty (@Nirvaan05) — lead contributor, maintainer

Contributing

Open an issue or PR. uv sync --all-extras && uv run pytest tests/ is all the setup you need to run the suite. Version bumps must update both pyproject.toml and npm/package.json and they must agree.

Vannevar Bush, 1945: "Consider a future device for individual use, which is a sort of mechanized private file and library. It needs a name, and to coin one at random, memex will do."